Whooping cough is caused by an infection of the respiratory tract with Bordetella pertussis bacteria. This disease is effectively controlled by the current vaccine which consists of killed whole B. pertussis cells. Though efficacious, the present vaccine produces unacceptable side effects. The major protective antigen in whooping cough vaccines is pertussis toxin. Clinical trials of acellular pertussis products strongly indicate that pertussis toxin will be a necessary and perhaps sufficient component of any new vaccine. Chemically "inactivated" pertussis toxin vaccines have been produced with reduced side effects and reasonable efficacy, however, residual activity may exist. Through our gene expression experiments we discovered a molecular approach for inactivation of pertussis toxin. Using site-specific DNA mutagenesis, the S1 subunit was modified by a single amino acid substitution. This mutation virtually eliminated toxic activity, yet the immunogenic protective epitope was retained. Other double amino acid substitutions are being evaluated. We have devised several methods to transfer these genetic changes into the chromosome of B. pertussis. Using these new mutant strains, a genetically detoxified pertussis toxin molecule has been produced. This nontoxic holotoxin has strong immunoprotective properties and can be used as a vaccine antigen without chemical inactivation.